Co-author Professor Alan Cooper, of the University of Adelaide says the debate over the origin of chickens in South America is important to understanding contact between early Americans and Polynesians.

One theory suggests they were introduced to South America by the Spanish conquistadors in the 15th century after the continent's "discovery" by Christopher Columbus.

However, a 2007 study by University of Auckland anthropologist Dr Alice Storey claims a chicken bone found in an archaeological site on the west coast of Chile proves pre-Columbian contact between Polynesians and indigenous South Americans.

Rare mutation

Storey's team found the chicken bone, which they carbon dated to around 600 years old, carried a rare mutation similar to chicken bones found in two prehistoric sites in the Pacific: Mele Havea in Tonga, and an island in American Samoa.

However, Cooper's team says the rare mutation is actually the most common genetic sequence found in chickens, called the "KFC" gene.

The group has shown this, he says, by using DNA data from 41 native Chilean chickens and comparing them with a publicly available database of 1000 domestic chicken sequences from across the world.

They also compared these with the published Chilean and Polynesian ancient DNA sequences.

"We consider the clustering of the modern Chilean chicken sequences with [groupings] predominant in Europe to indicate the contribution of Spanish-introduced chickens," they write.

'Controversial'

Cooper says it would be "controversial" to use "the single pre-Columbian sequence" as evidence for a Polynesian origin for chickens as Storey has done.

But, the director of the Australian Centre for Ancient DNA says their analysis did reveal that ancient chicken remains from Easter Island had a DNA sequence that originated from Indonesia or the Philippines.

"The ancient Easter Island specimens are clearly pre-European ... indicating that this haplotype [or grouping] must form part of the original Polynesian/Pacific chicken dispersal," the team writes.

"Because Easter Island is commonly suggested as the key site to facilitate contact between Polynesian and South American cultures, it is significant that the common Easter Island haplotypes do not appear to have reached South America or have not survived into the modern day if they did so."

The group also raises questions about the accuracy of carbon dating used in the original study.

Cooper says the site where the chicken bone was found at El Arenal in Chile was less than three kilometres from the sea.

He says, Storey and colleagues did not correct their carbon dating of the bone's age for possible marine carbon offset.

Marine carbon offset is the carbon embedded in the ocean and marine-derived foods.

They say the site where the bone was found had large shell middens suggesting the diet of the chicken was likely to contain materials from the ocean.

"If the diet of the El Arenal chicken included a marine carbon contribution of more than 20%, the calibrated aged would be post-Columbian," Cooper says.

New data supports original claim

Storey rejects the group's assertions and stands by the age of the ancient El Arenal chicken bone.

"The date is consistent with other dates from the site which was abandoned before any European, or their chickens, ever set foot in the Americas," she says.

"There are no European artefacts at the site so no suggestion the dates should be later."

Storey says she will soon publish supporting data based on two new chickens from the site.

"These show without any doubt there is no marine correction required," she says.

Storey says it is common sense that chickens worldwide share some DNA sequences as all chickens were domesticated and originated in Asia.

"We would absolutely expect all chickens, everywhere in the world, to have an Indian/Asian genetic signature as all chickens must come from one of those places.

"However, there was probably more than one region in which chickens were domesticated, like India, China or Thailand.

"This means that all chickens everywhere in the world have a mtDNA (mitochondrial DNA) signature that relates back to their Asian great, great ... grandmothers, and those will differ depending on the domestication centre."

She says Cooper's study shows the drawback of using only modern DNA to infer ancient or historic relationships.

"The maternal lineages [mtDNA] of domesticated animals have been manipulated by breeders for many years - so modern chickens are a mixed lot.

"If you really want to understand what lineages are in a given place at any point in time, you need to study the ancient DNA from dated archaeological remains."